Variant report

Variant	rs3888004
Chromosome Location	chr15:74468766-74468767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74468445..74470531-chr15:74504277..74507153,2	MCF-7	breast:
2	chr15:74466900..74472644-chr15:74474380..74478364,5	K562	blood:
3	chr15:74466900..74472029-chr15:74474380..74478364,5	K562	blood:
4	chr15:74467637..74470186-chr15:74471128..74474134,3	K562	blood:
5	chr15:74465639..74467443-chr15:74467856..74470686,2	MCF-7	breast:
6	chr15:74465289..74467713-chr15:74468699..74473006,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261543	Chromatin interaction
ENSG00000137868	Chromatin interaction
ENSG00000129009	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11630317	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11630924	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs11631509	0.85[EUR][1000 genomes]
rs11631944	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11639090	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11639369	0.82[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs11854957	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11855667	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs11857410	0.82[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs12899173	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12907503	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12911581	0.84[EUR][1000 genomes]
rs12912258	0.82[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs12912578	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12913041	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12915891	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs13259	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2062309	0.98[EUR][1000 genomes]
rs2415169	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2899824	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34147822	0.88[EUR][1000 genomes]
rs34573746	0.88[EUR][1000 genomes]
rs34868798	0.99[EUR][1000 genomes]
rs351242	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs35255788	0.88[EUR][1000 genomes]
rs35462746	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35661273	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3848160	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3848161	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs409856	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5742915	1.00[CHD][hapmap]
rs62003660	0.88[EUR][1000 genomes]
rs62003661	0.85[EUR][1000 genomes]
rs62005707	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62005709	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62005710	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62005711	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71399778	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs733163	0.82[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs8037531	0.91[CEU][hapmap];0.98[EUR][1000 genomes]
rs923118	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.99[EUR][1000 genomes]
rs9630417	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.98[EUR][1000 genomes]
rs971755	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs971756	0.82[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs971757	0.82[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833053	chr15:74360156-74555140	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1050884	chr15:74394983-74489413	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv904345	chr15:74458181-74526596	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv904346	chr15:74458181-74548773	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv904347	chr15:74462629-74537101	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv904348	chr15:74462629-74542686	Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3888004	C15orf39	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74464800-74473600	Enhancers	Right Ventricle	heart
2	chr15:74465000-74470000	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr15:74465200-74469200	Weak transcription	Aorta	Aorta
4	chr15:74465200-74472200	Weak transcription	Brain Substantia Nigra	brain
5	chr15:74465200-74473000	Enhancers	Brain Germinal Matrix	brain
6	chr15:74466000-74468800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr15:74466000-74468800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr15:74466000-74470000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:74466000-74472000	Enhancers	Placenta	Placenta
10	chr15:74466200-74468800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:74466200-74468800	Weak transcription	Brain Hippocampus Middle	brain
12	chr15:74466200-74471600	Weak transcription	Brain Anterior Caudate	brain
13	chr15:74466200-74492800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr15:74466400-74468800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:74466600-74470000	Weak transcription	Left Ventricle	heart
16	chr15:74466600-74473200	Enhancers	HSMMtube	muscle
17	chr15:74466600-74480600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr15:74466800-74469000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr15:74466800-74469800	Weak transcription	Fetal Heart	heart
20	chr15:74467200-74469000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr15:74467200-74469200	Weak transcription	A549	lung
22	chr15:74467200-74471000	Enhancers	Fetal Brain Female	brain
23	chr15:74467200-74473600	Enhancers	Right Atrium	heart
24	chr15:74467400-74469000	Weak transcription	NHLF	lung
25	chr15:74467400-74469000	Weak transcription	Osteobl	bone
26	chr15:74467400-74469400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
27	chr15:74467400-74471200	Weak transcription	Fetal Thymus	thymus
28	chr15:74467400-74471600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr15:74467400-74472200	Weak transcription	Pancreas	Pancrea
30	chr15:74467400-74473400	Genic enhancers	Fetal Stomach	stomach
31	chr15:74467400-74473800	Enhancers	NHDF-Ad	bronchial
32	chr15:74467600-74469400	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
33	chr15:74467600-74469400	Transcr. at gene 5' and 3'	Ovary	ovary
34	chr15:74467600-74473200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:74467800-74469600	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
36	chr15:74467800-74470200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:74467800-74472400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:74467800-74473600	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr15:74468000-74468800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr15:74468000-74471600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr15:74468000-74472200	Weak transcription	Gastric	stomach
42	chr15:74468200-74469200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:74468200-74469400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr15:74468200-74470200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:74468200-74471000	Enhancers	Fetal Lung	lung
46	chr15:74468400-74468800	Enhancers	Adipose Nuclei	Adipose
47	chr15:74468400-74468800	Weak transcription	Esophagus	oesophagus
48	chr15:74468400-74468800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
49	chr15:74468400-74469400	Weak transcription	Fetal Intestine Small	intestine
50	chr15:74468400-74469400	Enhancers	Lung	lung

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